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This page was generated on 2021-10-15 15:06:01 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the CoRegFlux package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CoRegFlux.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 391/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pauline Trébulle and Mohamed Elati
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: CoRegFlux |
| Version: 1.8.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoRegFlux.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CoRegFlux_1.8.0.tar.gz |
| StartedAt: 2021-10-14 21:35:55 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:40:28 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 273.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: CoRegFlux.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoRegFlux.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CoRegFlux_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CoRegFlux.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CoRegFlux/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CoRegFlux' version '1.8.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CoRegFlux' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'CoRegFlux' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CoRegFlux.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
predict_linear_model_influence 19.95 0.2 20.16
Simulation 5.62 0.2 6.01
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
predict_linear_model_influence 19.74 0.27 20.03
Simulation 5.54 0.07 5.80
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'Test.R'
ERROR
Running the tests in 'tests/Test.R' failed.
Last 13 lines of output:
Error in `convert_metabolites_to_model_names(metabolites = metabolites,
model = iMM904)`: could not find function "convert_metabolites_to_model_names"
Backtrace:
1. testthat::expect_true(...) test_MetabolicModelFunctions.R:13:5
4. base::is.data.frame(...)
--------------------------------------------------------------------------------
== Results =====================================================================
Duration: 43.0 s
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 29 ]
Don't worry, you'll get it.
Error: Test failures
Execution halted
** running tests for arch 'x64' ...
Running 'Test.R'
ERROR
Running the tests in 'tests/Test.R' failed.
Last 13 lines of output:
Error (test_MetabolicModelFunctions.R:13:6): Metabolites names to model names works and return a
data.frame
Error in `convert_metabolites_to_model_names(metabolites = metabolites,
model = iMM904)`: could not find function "convert_metabolites_to_model_names"
Backtrace:
1. testthat::expect_true(...) test_MetabolicModelFunctions.R:13:5
4. base::is.data.frame(...)
--------------------------------------------------------------------------------
== Results =====================================================================
Duration: 44.1 s
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 WARNING
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/CoRegFlux.Rcheck/00check.log'
for details.
CoRegFlux.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CoRegFlux_1.8.0.tar.gz && rm -rf CoRegFlux.buildbin-libdir && mkdir CoRegFlux.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoRegFlux.buildbin-libdir CoRegFlux_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CoRegFlux_1.8.0.zip && rm CoRegFlux_1.8.0.tar.gz CoRegFlux_1.8.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
16 4573k 16 748k 0 0 1975k 0 0:00:02 --:--:-- 0:00:02 1975k
95 4573k 95 4386k 0 0 3172k 0 0:00:01 0:00:01 --:--:-- 3171k
100 4573k 100 4573k 0 0 3217k 0 0:00:01 0:00:01 --:--:-- 3218k
install for i386
* installing *source* package 'CoRegFlux' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CoRegFlux'
finding HTML links ... done
FBA_step html
ODCurveToFluxCurves html
ODCurveToMetabolicGeneCurves html
ODToFluxBounds html
ODcurveToMetCurve html
ODtoflux html
PredictedGeneState html
SC_EXP_DATA html
SC_GRN_1 html
SC_Test_data html
SC_experiment_influence html
Simulation html
Simulation_Step html
adjust_constraints_to_observed_rates html
aliases_SC html
build_exchange_met html
continuous_gpr html
convert_metabolites_to_model_names html
coregflux_static html
euler_step_biomass html
euler_step_metabolites html
get_biomass_flux_position html
get_fba_fluxes_from_observations html
get_fva_intervals_from_observations html
get_linear_model html
get_metabolites_exchange_fluxes html
gpr_expression html
iMM904 html
perturbation_function html
predict_linear_model_influence html
train_continuous_model html
update_fluxes_constraints_GRegulation html
update_fluxes_constraints_geneKOOV html
update_fluxes_constraints_influence html
update_fluxes_state html
update_system_state html
update_uptake_fluxes_constraints_metabolites
html
visFluxCurves html
visMetabolicGeneCurves html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'CoRegFlux' is deprecated and will be removed from Bioconductor
version 3.14
** testing if installed package can be loaded from final location
Warning: Package 'CoRegFlux' is deprecated and will be removed from Bioconductor
version 3.14
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'CoRegFlux' ...
** testing if installed package can be loaded
Warning: Package 'CoRegFlux' is deprecated and will be removed from Bioconductor
version 3.14
* MD5 sums
packaged installation of 'CoRegFlux' as CoRegFlux_1.8.0.zip
* DONE (CoRegFlux)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CoRegFlux' successfully unpacked and MD5 sums checked
|
CoRegFlux.Rcheck/tests_i386/Test.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(CoRegFlux)
Warning message:
Package 'CoRegFlux' is deprecated and will be removed from Bioconductor
version 3.14
> library(testthat)
>
> testthat::test_dir("testthat/")
v | F W S OK | Context
/ | 0 | CoregfluxAndFVAFunctions
/ | 0 | CoregfluxAndFVAFonctions
- | 1 | CoregfluxAndFVAFonctions
| | 3 | CoregfluxAndFVAFonctions
v | 6 | CoregfluxAndFVAFonctions [40.6s]
/ | 0 | DFBAsimulationFunctions
/ | 0 | DFBAsimulationFunctions
- | 1 | DFBAsimulationFunctions
/ | 3 5 | DFBAsimulationFunctions
x | 3 17 | DFBAsimulationFunctions [2.2s]
--------------------------------------------------------------------------------
Error (test_DFBAsimulationFunctions.R:41:6): uptake fluxes diminish metabolite concentrations
Error in `euler_step_metabolites(met_concentrations_t0 = 10, fluxes = -1,
rate = 0.1, time_step = 0.1, biomass_t0 = 0.3)`: could not find function "euler_step_metabolites"
Backtrace:
1. testthat::expect_lt(...) test_DFBAsimulationFunctions.R:41:5
2. testthat::quasi_label(enquo(object), label, arg = "object")
3. rlang::eval_bare(expr, quo_get_env(quo))
Error (test_DFBAsimulationFunctions.R:49:6): positive fluxes increase metabolite concentrations
Error in `euler_step_metabolites(met_concentrations_t0 = 10, fluxes = 1,
rate = 0.1, time_step = 0.1, biomass_t0 = 0.3)`: could not find function "euler_step_metabolites"
Backtrace:
1. testthat::expect_gt(...) test_DFBAsimulationFunctions.R:49:5
2. testthat::quasi_label(enquo(object), label, arg = "object")
3. rlang::eval_bare(expr, quo_get_env(quo))
Error (test_DFBAsimulationFunctions.R:59:16): update_uptake_fluxes_constraints_metabolites check that
bounds are changed
Error in `update_uptake_fluxes_constraints_metabolites(model = iMM904,
met_fluxes_indexes = 550, biomass_t0 = 0.3, met_concentrations_t0 = 1e-06,
time_step = 1)`: could not find function "update_uptake_fluxes_constraints_metabolites"
--------------------------------------------------------------------------------
/ | 0 | MetabolicModelFunctions
/ | 0 | MetabolicModelFunctions
- | 1 0 | MetabolicModelFunctions
x | 1 6 | MetabolicModelFunctions [0.1s]
--------------------------------------------------------------------------------
Error (test_MetabolicModelFunctions.R:13:6): Metabolites names to model names works and return a
data.frame
Error in `convert_metabolites_to_model_names(metabolites = metabolites,
model = iMM904)`: could not find function "convert_metabolites_to_model_names"
Backtrace:
1. testthat::expect_true(...) test_MetabolicModelFunctions.R:13:5
4. base::is.data.frame(...)
--------------------------------------------------------------------------------
== Results =====================================================================
Duration: 43.0 s
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 29 ]
Don't worry, you'll get it.
Error: Test failures
Execution halted
|
CoRegFlux.Rcheck/tests_x64/Test.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(CoRegFlux)
Warning message:
Package 'CoRegFlux' is deprecated and will be removed from Bioconductor
version 3.14
> library(testthat)
>
> testthat::test_dir("testthat/")
v | F W S OK | Context
/ | 0 | CoregfluxAndFVAFunctions
/ | 0 | CoregfluxAndFVAFonctions
- | 1 | CoregfluxAndFVAFonctions
| | 3 | CoregfluxAndFVAFonctions
v | 6 | CoregfluxAndFVAFonctions [41.6s]
/ | 0 | DFBAsimulationFunctions
/ | 0 | DFBAsimulationFunctions
- | 1 | DFBAsimulationFunctions
/ | 3 5 | DFBAsimulationFunctions
/ | 3 13 | DFBAsimulationFunctions
x | 3 17 | DFBAsimulationFunctions [2.3s]
--------------------------------------------------------------------------------
Error (test_DFBAsimulationFunctions.R:41:6): uptake fluxes diminish metabolite concentrations
Error in `euler_step_metabolites(met_concentrations_t0 = 10, fluxes = -1,
rate = 0.1, time_step = 0.1, biomass_t0 = 0.3)`: could not find function "euler_step_metabolites"
Backtrace:
1. testthat::expect_lt(...) test_DFBAsimulationFunctions.R:41:5
2. testthat::quasi_label(enquo(object), label, arg = "object")
3. rlang::eval_bare(expr, quo_get_env(quo))
Error (test_DFBAsimulationFunctions.R:49:6): positive fluxes increase metabolite concentrations
Error in `euler_step_metabolites(met_concentrations_t0 = 10, fluxes = 1,
rate = 0.1, time_step = 0.1, biomass_t0 = 0.3)`: could not find function "euler_step_metabolites"
Backtrace:
1. testthat::expect_gt(...) test_DFBAsimulationFunctions.R:49:5
2. testthat::quasi_label(enquo(object), label, arg = "object")
3. rlang::eval_bare(expr, quo_get_env(quo))
Error (test_DFBAsimulationFunctions.R:59:16): update_uptake_fluxes_constraints_metabolites check that
bounds are changed
Error in `update_uptake_fluxes_constraints_metabolites(model = iMM904,
met_fluxes_indexes = 550, biomass_t0 = 0.3, met_concentrations_t0 = 1e-06,
time_step = 1)`: could not find function "update_uptake_fluxes_constraints_metabolites"
--------------------------------------------------------------------------------
/ | 0 | MetabolicModelFunctions
/ | 0 | MetabolicModelFunctions
- | 1 0 | MetabolicModelFunctions
x | 1 6 | MetabolicModelFunctions [0.1s]
--------------------------------------------------------------------------------
Error (test_MetabolicModelFunctions.R:13:6): Metabolites names to model names works and return a
data.frame
Error in `convert_metabolites_to_model_names(metabolites = metabolites,
model = iMM904)`: could not find function "convert_metabolites_to_model_names"
Backtrace:
1. testthat::expect_true(...) test_MetabolicModelFunctions.R:13:5
4. base::is.data.frame(...)
--------------------------------------------------------------------------------
== Results =====================================================================
Duration: 44.1 s
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted
|
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CoRegFlux.Rcheck/examples_i386/CoRegFlux-Ex.timings
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CoRegFlux.Rcheck/examples_x64/CoRegFlux-Ex.timings
|